Just seen your problem and joined so I could answer, I had exactly the same issue and I have the BG HD Freeview dual tuner installed.
After months of playing and changing my ariel I could never figure out why my tele was fine yet my freeview card played up in MCE.
Firstly I went here Freeview on The Wrekin TV transmitter | ukfree.tv - independent free digital TV advice
and found out what transmitter I was supposed to be receiving from, as you can see I am using the Wrekin transmitter.
If you scroll down you will see the correct frequency that you need to tune to for specific channels, so for me bbc1 is on 514.0MHz
Now on mediacentre go to settings-tv-guide-edit channels
select a channel (bbc1 in this example), scroll down the options on the left to "Edit Sources". Here you will see all the frequencies MCE pickup during the scan, note there is a record for each frequency for each tuner so in bbc1 I have 18! yes 18 sources which is 9 for each tuner 9 x 2 = 18 obviously.
Simply scroll through the list and enable the options that fit your transmitter (in my case 514.0MHz twice) I also use the arrows on the menu to make them no's 1 & 2 in the list to make sure they are the highest priority.
Unfortunaltly you have to do this for all channels but it is worth the time investment.
From what I could gather MCE will try and select the frequency that has 100% quality but this seems to fail and did for me on the ITV main channels as it trying to tune to a transmitter I was not pointing at.
After setting all my channels (with a quality of 60% showing in MCE) it has been fine with no breakup and after months of digging I found my answer
I hope this helps